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https://www.readbyqxmd.com/read/27913635/screening-and-analysis-of-janelia-flylight-project-enhancer-gal4-strains-identifies-multiple-gene-enhancers-active-during-hematopoiesis-in-normal-and-wasp-challenged-drosophila-larvae
#1
Tsuyoshi Tokusumi, Yumiko Tokusumi, Mark S Brahier, Victoria Lam, Jessica R Stoller-Conrad, Paul T Kroeger, Robert A Schulz
A GFP expression screen has been conducted on greater than one thousand Janelia FlyLight Project enhancer-Gal4 lines to identify transcriptional enhancers active in the larval hematopoietic system. A total of 190 enhancers associated with 87 distinct genes showed activity in cells of the third instar larval lymph gland and hemolymph. That is, gene enhancers were active in cells of the lymph gland posterior signaling center (PSC), medullary zone (MZ), and/or cortical zone (CZ), while certain of the transcriptional control regions were active in circulating hemocytes...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27910922/the-influence-of-laser-scribing-on-magnetic-domain-formation-in-grain-oriented-electrical-steel-visualized-by-directional-neutron-dark-field-imaging
#2
P Rauscher, B Betz, J Hauptmann, A Wetzig, E Beyer, C Grünzweig
The performance and degree of efficiency of transformers are directly determined by the bulk magnetic properties of grain oriented electrical steel laminations. The core losses can be improved by post manufacturing methods, so-called domain refinement techniques. All these methods induce mechanical or thermal stress that refines the domain structure. The most commonly used technique is laser scribing due to the no-contact nature and the ease of integration in existing production systems. Here we show how directional neutron dark-field imaging allows visualizing the impact of laser scribing on the bulk and supplementary domain structure...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910777/gastric-adenocarcinoma-biomarker-expression-profiles-and-their-prognostic-value
#3
Serkan Senol, Abdullah Aydin, Duygu Kosemetin, Dilek Ece, Ibrahim Akalin, Hasan Abuoglu, Esra Akdeniz Duran, Dincer Aydin, Burcak Erkol
Expression levels of several molecules implicated in carcinogenesis were examined by immunohistochemical staining, and the prognostic significance of their expression levels in gastric adenocarcinoma (GA) was evaluated. A total of 115 GA and 20 control gastric tissue samples were evaluated by immunohistochemistry using 33 antibodies targeting molecules known to play a part in the development of various tumors. Overexpression of carbonic anhydrase IX (CAIX) and loss of AT-rich interactive domain-containing protein 1A (ARID1A), aldehyde dehydrogenase 1 (ALDH1), and CD44 expression in GA patients were significantly correlated with lymph node (LN) metastasis, advanced tumor stage, and poor prognosis...
2016: Journal of Environmental Pathology, Toxicology and Oncology
https://www.readbyqxmd.com/read/27909398/an-amyloid-like-pathological-conformation-of-tdp-43-is-stabilized-by-hypercooperative-hydrogen-bonds
#4
Miguel Mompeán, Marco Baralle, Emanuele Buratti, Douglas V Laurents
TDP-43 is an essential RNA-binding protein forming aggregates in almost all cases of sporadic amyotrophic lateral sclerosis (ALS) and many cases of frontotemporal lobar dementia (FTLD) and other neurodegenerative diseases. TDP-43 consists of a folded N-terminal domain with a singular structure, two RRM RNA-binding domains, and a long disordered C-terminal region which plays roles in functional RNA regulatory assemblies as well as pernicious aggregation. Evidence from pathological mutations and seeding experiments strongly suggest that TDP-43 aggregates are pathologically relevant through toxic gain-of-harmful-function and/or harmful loss-of-native-function mechanisms...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27909246/retromer-wash-dependent-sorting-of-nutrient-transporters-requires-a-multivalent-interaction-network-with-ankrd50
#5
Arunas Kvainickas, Ana Jimenez Orgaz, Heike Nägele, Britta Diedrich, Kate J Heesom, Jörn Dengjel, Peter J Cullen, Florian Steinberg
Retromer and the associated actin polymerizing WASH-complex are essential for the endocytic recycling of a wide range of integral membrane proteins. A hereditary Parkinson's disease causing point mutation (D620N) in the retromer subunit VPS35 perturbs retromer's association with the WASH-complex and also with the uncharacterized protein Ankyrin Repeat Domain Containing Protein 50 (ANKRD50). Here, we firmly establish ANKRD50 as a novel and essential component of the SNX27-retromer-WASH supercomplex. Depletion of ANKRD50 in HeLa or U2OS cells phenocopied the loss of endosome to cell surface recycling of multiple transmembrane proteins seen upon suppression of SNX27, retromer or WASH-complex components...
December 1, 2016: Journal of Cell Science
https://www.readbyqxmd.com/read/27909050/notch-pathway-is-activated-via-genetic-and-epigenetic-alterations-and-is-a-therapeutic-target-in-clear-cell-renal-cancer
#6
Tushar D Bhagat, Yiyu Zou, Shizeng Huang, Jihwan Park, Matthew B Palmer, Caroline Hu, Wejuan Li, Niraj Shenoy, Orsolya Giricz, Gaurav Choudhary, Yiting Yu, Yi-An Ko, Maria C Izquierdo, Ae Seo Deok Park, Nishanth Vallumsetla, Remi Laurence, Robert Lopez, Masako Suzuki, James Pullman, Justin Kaner, Benjamin Gartrell, A Ari Hakimi, John M Greally, Bharvin Patel, Karim Benhadji, Kith Pradhan, Amit Verma, Katalin Susztak
Clear cell renal cell carcinoma (CCRCC) is an incurable malignancy in advanced stages and needs newer therapeutic targets. Transcriptomic analysis of CCRCCs and matched microdissected renal tubular controls revealed overexpression of NOTCH ligands and receptors in tumor tissues. Examination of the TCGA RNA-seq dataset also revealed widespread activation of NOTCH pathway in a large cohort of CCRCC samples. Samples with NOTCH pathway activation were also clinically distinct and were associated with better overall survival...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27908033/an-axisymmetric-time-domain-spectral-element-method-for-full-wave-simulations-application-to-ocean-acoustics
#7
Alexis Bottero, Paul Cristini, Dimitri Komatitsch, Mark Asch
The numerical simulation of acoustic waves in complex three-dimensional (3D) media is a key topic in many branches of science, from exploration geophysics to non-destructive testing and medical imaging. With the drastic increase in computing capabilities this field has dramatically grown in the last 20 years. However many 3D computations, especially at high frequency and/or long range, are still far beyond current reach and force researchers to resort to approximations, for example, by working in two dimensions (plane strain) or by using a paraxial approximation...
November 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27908012/pt-symmetric-couplers-with-competing-cubic-quintic-nonlinearities
#8
Gennadiy Burlak, Salomon Garcia-Paredes, Boris A Malomed
We introduce a one-dimensional model of the parity-time ( PT)-symmetric coupler, with mutually balanced linear gain and loss acting in the two cores, and nonlinearity represented by the combination of self-focusing cubic and defocusing quintic terms in each core. The system may be realized in optical waveguides, in the spatial and temporal domains alike. Stationary solutions for PT-symmetric solitons in the systems are tantamount to their counterparts in the ordinary coupler with the cubic-quintic nonlinearity, where the spontaneous symmetry breaking of solitons is accounted for by bifurcation loops...
November 2016: Chaos
https://www.readbyqxmd.com/read/27905926/understanding-clinical-and-non-clinical-decisions-under-uncertainty-a-scenario-based-survey
#9
Vlad V Simianu, Margaret A Grounds, Susan L Joslyn, Jared E LeClerc, Anne P Ehlers, Nidhi Agrawal, Rafael Alfonso-Cristancho, Abraham D Flaxman, David R Flum
BACKGROUND: Prospect theory suggests that when faced with an uncertain outcome, people display loss aversion by preferring to risk a greater loss rather than incurring certain, lesser cost. Providing probability information improves decision making towards the economically optimal choice in these situations. Clinicians frequently make decisions when the outcome is uncertain, and loss aversion may influence choices. This study explores the extent to which prospect theory, loss aversion, and probability information in a non-clinical domain explains clinical decision making under uncertainty...
December 1, 2016: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/27903803/the-human-cytomegalovirus-ie1-protein-antagonizes-pml-nuclear-body-mediated-intrinsic-immunity-via-the-inhibition-of-pml-de-novo-sumoylation
#10
Eva-Maria Schilling, Myriam Scherer, Nina Reuter, Johannes Schweininger, Yves A Muller, Thomas Stamminger
: PML nuclear bodies (NBs) are accumulations of cellular proteins embedded in a scaffold-like structure built by SUMO-modified PML/TRIM19. PML and other NB proteins act as cellular restriction factors against human cytomegalovirus (HCMV), however, this intrinsic defense is counteracted by the immediate-early protein 1 (IE1) of HCMV. IE1 directly interacts with the PML coiled-coil domain via its globular core region and disrupts NB foci by inducing a loss of PML SUMOylation. Here, we demonstrate that IE1 acts via abrogating the de novo SUMOylation of PML...
November 30, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27903652/prepore-stability-controls-productive-folding-of-the-bam-independent-multimeric-outer-membrane-secretin-puld
#11
Ingrid Guilvout, Sébastien Brier, Mohamed Chami, Véronique Hourdel, Olivera Francetic, Anthony P Pugsley, Julia Chamot-Rooke, Gerard H M Huysmans
Members of a group of multimeric secretion pores that assemble independently of any known membrane-embedded insertase in Gram-negative bacteria fold into a prepore before membrane-insertion occurs. The mechanisms and the energetics that drive the folding of these proteins are poorly understood. Here, equilibrium unfolding and hydrogen/deuterium exchange monitored by mass spectrometry indicated that a loss of 4-5 kJ/mol/protomer in the N3-domain that is peripheral to the membrane-spanning C-domain in the dodecameric secretin PulD, the founding member of this class, prevents pore formation by destabilizing the prepore into a poorly structured dodecamer as visualized by electron microscopy...
November 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27902541/central-serous-chorioretinopathylike-mimicking-multifocal-vitelliform-macular-dystrophy-an-ocular-side-effect-of-mitogen-extracellular-signal-regulated-kinase-inhibitors
#12
Chiara Giuffrè, Elisabetta Miserocchi, Giulio Modorati, Adriano Carnevali, Alessandro Marchese, Lea Querques, Giuseppe Querques, Francesco Bandello
PURPOSE: To describe a case of multiple detachments of the neurosensory retina mimicking multifocal vitelliform macular dystrophy after chemotherapy with mitogen/extracellular signal-regulated kinase inhibitor for metastatic ovarian cancer. METHODS: Case report. RESULTS: A 38-year-old woman presented to our clinic for eye examination before the initiation of chemotherapy with trametinib. One month after starting treatment, the patient complained of vision loss and metamorphopsia in both eyes...
November 29, 2016: Retinal Cases & Brief Reports
https://www.readbyqxmd.com/read/27902397/vesivirus-2117-capsids-more-closely-resemble-sapovirus-and-lagovirus-particles-than-other-known-vesivirus-structures
#13
Michaela Conley, Edward Emmott, Richard Orton, David Taylor, Daniel Carneiro, Kazuyoshi Murata, Ian Goodfellow, Grant Hansman, David Bhella
Vesivirus 2117 is an adventitious agent that in 2009, was identified as a contaminant of CHO cells propagated in bioreactors at a pharmaceutical manufacturing plant belonging to Genzyme. The consequent interruption in supply of Fabrazyme and Cerezyme (drugs used to treat Fabry and Gaucher disease respectively), caused significant economic losses. Vesivirus 2117 is a member of the Caliciviridae; a family of small icosahedral viruses encoding a positive sense RNA genome. We have used cryo-electron microscopy and three dimensional image reconstruction to calculate a structure of vesivirus 2117 virus like particles as well as feline calicivirus and a chimeric sapovirus...
November 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27902320/in-silico-analysis-of-surface-structure-variation-of-pcv2-capsid-resulted-from-loops-mutation-of-its-capsid-protein-cap
#14
Naidong Wang, Yang Zhan, Aibing Wang, Lijie Zhang, Reza Khayat, Yi Yang
Outbreaks of porcine circovirus (PCV) type 2 (PCV2) associated diseases (PCVADs) have caused substantial economic losses worldwide in the last 20 y. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees constructed, but variation of surface structure of the PCV capsid were analyzed in the course of evolution. Unique surface patterns of the icosahedral 5-fold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1)...
October 18, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901048/sparsity-based-multi-height-phase-recovery-in-holographic-microscopy
#15
Yair Rivenson, Yichen Wu, Hongda Wang, Yibo Zhang, Alborz Feizi, Aydogan Ozcan
High-resolution imaging of densely connected samples such as pathology slides using digital in-line holographic microscopy requires the acquisition of several holograms, e.g., at >6-8 different sample-to-sensor distances, to achieve robust phase recovery and coherent imaging of specimen. Reducing the number of these holographic measurements would normally result in reconstruction artifacts and loss of image quality, which would be detrimental especially for biomedical and diagnostics-related applications...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900366/exome-sequencing-reveals-germline-gain-of-function-egfr-mutation-in-an-adult-with-lhermitte-duclos-disease
#16
Samantha Colby, Lamis Yehia, Farshad Niazi, JinLian Chen, Ying Ni, Jessica L Mester, Charis Eng
Lhermitte-Duclos disease (LDD) is a rare cerebellar disorder believed to be pathognomonic for Cowden syndrome. Presently, the only known etiology is germline PTEN mutation. We report a 41-yr-old white female diagnosed with LDD and wild-type for PTEN. Exome sequencing revealed a germline heterozygous EGFR mutation that breaks a disulfide bond in the receptor's extracellular domain, resulting in constitutive activation. Functional studies demonstrate activation of ERK/AKT signaling pathways, mimicking PTEN loss-of-function downstream effects...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27900362/de-novo-phip-predicted-deleterious-variants-are-associated-with-developmental-delay-intellectual-disability-obesity-and-dysmorphic-features
#17
Emily Webster, Megan T Cho, Nora Alexander, Sonal Desai, Sakkubai Naidu, Mir Reza Bekheirnia, Andrea Lewis, Kyle Retterer, Jane Juusola, Wendy K Chung
Using whole-exome sequencing, we have identified novel de novo heterozygous pleckstrin homology domain-interacting protein (PHIP) variants that are predicted to be deleterious, including a frameshift deletion, in two unrelated patients with common clinical features of developmental delay, intellectual disability, anxiety, hypotonia, poor balance, obesity, and dysmorphic features. A nonsense mutation in PHIP has previously been associated with similar clinical features. Patients with microdeletions of 6q14.1, including PHIP, have a similar phenotype of developmental delay, intellectual disability, hypotonia, and obesity, suggesting that the phenotype of our patients is a result of loss-of-function mutations...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27899926/bioinformatic-analyses-of-subgroup-a-members-of-the-wheat-bzip-transcription-factor-family-and-functional-identification-of-tabzip174-involved-in-drought-stress-response
#18
Xueyin Li, Biane Feng, Fengjie Zhang, Yimiao Tang, Liping Zhang, Lingjian Ma, Changping Zhao, Shiqing Gao
Extensive studies in Arabidopsis and rice have demonstrated that Subgroup-A members of the bZIP transcription factor family play important roles in plant responses to multiple abiotic stresses. Although common wheat (Triticum aestivum) is one of the most widely cultivated and consumed food crops in the world, there are limited investigations into Subgroup A of the bZIP family in wheat. In this study, we performed bioinformatic analyses of the 41 Subgroup-A members of the wheat bZIP family. Phylogenetic and conserved motif analyses showed that most of the Subgroup-A bZIP proteins involved in abiotic stress responses of wheat, Arabidopsis, and rice clustered in Clade A1 of the phylogenetic tree, and shared a majority of conserved motifs, suggesting the potential importance of Clade-A1 members in abiotic stress responses...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27896646/improvement-of-health-related-quality-of-life-after-roux-en-y-gastric-bypass-related-to-weight-loss
#19
Valerie M Monpellier, Evangelia E Antoniou, Edo O Aarts, Ignace M C Janssen, Anita T M Jansen
INTRODUCTION: Effect of bariatric surgery on health-related quality of life (HRQOL) varies greatly. This might be caused by the diversity in questionnaires used to assess HRQOL and the weight loss of the studied population. This study assesses the relationship between weight loss and HRQOL in primary Roux-en-Y gastric bypass (RYGB) patients by using an obesity-specific (impact of weight on quality of life-lite, IWQOL-lite) and a generic (RAND-36) questionnaire. METHODS: HRQOL and weight parameters were assessed before and 15 and 24 months after RYGB surgery...
November 28, 2016: Obesity Surgery
https://www.readbyqxmd.com/read/27895300/thsd1-thrombospondin-type-1-domain-containing-protein-1-mutation-in-the-pathogenesis-of-intracranial-aneurysm-and-subarachnoid-hemorrhage
#20
Teresa Santiago-Sim, Xiaoqian Fang, Morgan L Hennessy, Stephen V Nalbach, Steven R DePalma, Ming Sum Lee, Steven C Greenway, Barbara McDonough, Georgene W Hergenroeder, Kyla J Patek, Sarah M Colosimo, Krista J Qualmann, John P Hagan, Dianna M Milewicz, Calum A MacRae, Susan M Dymecki, Christine E Seidman, J G Seidman, Dong H Kim
BACKGROUND AND PURPOSE: A ruptured intracranial aneurysm (IA) is the leading cause of a subarachnoid hemorrhage. This study seeks to define a specific gene whose mutation leads to disease. METHODS: More than 500 IA probands and 100 affected families were enrolled and clinically characterized. Whole exome sequencing was performed on a large family, revealing a segregating THSD1 (thrombospondin type 1 domain containing protein 1) mutation. THSD1 was sequenced in other probands and controls...
December 2016: Stroke; a Journal of Cerebral Circulation
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